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Characterization of phenotypic and genotypic selection for simple and complex traits of barley (Hordeum vulgare L.)

Gill, Reetinder (2009) Characterization of phenotypic and genotypic selection for simple and complex traits of barley (Hordeum vulgare L.). PhD thesis, Murdoch University.

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The challenge to modern day plant breeding is to constantly strive to improve the efficiency and efficacy of utilising the available resources. This requires the integration of conventional breeding technologies together with molecular genetic markers to significantly improve the breeding programs.
Male sterile facilitated recurrent selection (MSFRS) can improve a breeding program by reducing the variety release time to almost half, maintaining continued out-crossing and recombination, thus broadening the germplasm base. A molecular genetic marker system for the male sterile-orange lemma-shrunken endosperm (msg6-rob1-sex1) linkage block was developed during this study, to aid in the differentiation of fully fertile homozygous from fully fertile heterozygous plump individuals in F2 populations. These individuals may be desired for the production of doubled haploids or for use as pollen donor parents in further cycles of MSFRS. A DF578/6*Gairdner BC5 population was chosen for the study and SSR markers were identified in the region of the msg6-rob1-sex1 linkage group on the short arm of chromosome 6H. A linkage map was constructed and it was found that microsatellite markers HVM65, HVM74 and Bmgtttttt1 are tightly linked to msg6-rob1-sex1 linkage block.
Within the MSFRS process, it was found that genotypic selection with SSR markers is an advantage when the phenotype of interest is controlled by a single major gene and the marker is either “perfect” or closely linked. Genotypic selection was found to be very effective in selecting for the aluminium tolerant genotypes with the SSR marker HVM68, where aluminium tolerance is known to be controlled by Alt or Alp gene on chromosome 4H.
For the complex trait such as barley scald resistance, genotypic selection was found to be of limited value. Simulation studies demonstrated that multiple genetic factors need to be taken into account while selecting for a complex phenotype. As expected, phenotypic selection method was found to be efficient in selecting for scald resistance as it selected minor genes along with two known major genes for scald resistance on chromosome 4H (RhsVlamingh) and 6H (RhsWABAR2147).
Simulation studies based on the experimental results provided a guide for the frequency and timing of the use of molecular markers in the breeding program. It was found that markers that are loosely linked to the gene of interest should only be used once early in the breeding program. As in the case of scald resistance, where the markers-gene distances are 5cM or 30 cM, the genes can only be partially fixed. Further cycles of genotypic selection for scald resistance will lead to the selection of the susceptible genotypes instead of resistant genotypes as the phenotype comes in repulsion rather than the coupling phase with the scald resistant genes.
GGT (an acronym of Graphical GenoTypes) software package was extensively used to study genotypic changes in response to selection and to select for the genotypes carrying resistant genes of interest. Based on the allele frequencies and the marker-scald associations carried out using GGT, the SSR marker Bmac213 (1H) was found to be associated with powdery mildew (MlaWABAR2147) resistance and SSR markers GBM1221 (4H) and Bmac316 (6H) were found to be associated with scald (RhsVlamingh and RhsWABAR2147) resistance.
Results presented in this thesis have enabled the identification of mechanisms behind the success of phenotypic selection and its use while selecting for quantitative traits as it incorporates the minor gene effects while selecting for the major genes. Genotypic selection method was found to be efficient in selecting for the desired genotypes but may not give the desired result in terms of phenotype when a complex trait is involved. Genotypic selection will be at par with the phenotypic selection for the complex quantitative traits if the associated markers with the minor genes are included in the selection. Both phenotypic and genotypic selection methods together can be used effectively in the breeding program to increase the rate of genetic gain.

Item Type: Thesis (PhD)
Murdoch Affiliation(s): School of Biological Sciences and Biotechnology
Supervisor(s): Lance, Reg, Appels, Rudi and Li, Chengdao
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